Link to this post | posted 20 May, 2019 19:33

debbie

Dear SEA-PHAGES faculty, Have you see phage DNA appear as a smear on an agarose gel? There are particular instances in which DNA modification can lead to degradation in the gel buffers, such that even undigested genomic DNA appears as a smear. It’s possible that you’ve observed it but not necessarily submitted the DNA for sequencing. We would like to hear whether or not you’ve seen this. We’ve opened up a Forum at seaphagesdb.org, and would like to encourage you to indicate with which phages you saw this (with pictures if you have them) or point to a phage pages on phagesdb.org if the data are posted there. But we’d also like it if you could post a note saying that you have never seen this, if that is the case. If you have further questions, don’t hesitate to contact me. Thanks! debbie

Link to this post | posted 15 May, 2019 18:26

debbie

Sally, Technically, we can call a single TMD if 2 programs find it. I would not be opposed to calling them both Hypothetical Proteins. I just looked at these in phamerator. These 2 genes are found in a region of high nucleotide pairwise similarity (the purple color inbetween). However, the first of these 2 genes is a member of 3 different phams. Are they all calling different things, or is this a case of small genes not meeting alignment cut-offs to make it into the same pham? debbie

Link to this post | posted 07 May, 2019 19:19
debbie	Kristen, While I agree the currently called ribosomal slippage is not a stellar example, I don't think the placement of your proposed slippage works (because you are slipping out of the first frame too soon). I think we are approximately at the right place if there is indeed a frameshift. If you look at Powerball, the GGGGACT is not there…….. Kristen - I'll ask Welkin for her in put. debbie

Link to this post | posted 24 Apr, 2019 18:25

debbie

Christos, Try the following things, one may do the trick. If not send it to me and I will try to make it work. At the feature table, go to the left sequence tab. Once in the window, above the sequence, click on the button "raw". Recreate your documentation. Go to documentation, the click on recreate. Save the file as a new name and see if it works. If you do need my help, what is he trying to export? debbie

Link to this post | posted 19 Apr, 2019 18:45
debbie	Sara, Nope. Sorry for the confusion. I think that peak is a gene (7165-7272). I just have no confidence it is the T of the G/T frameshift, so I would not assign a function to it.

Link to this post | posted 18 Apr, 2019 13:27

debbie

Sara, This is a timely question. This summer Welkin learned that siphoviridae do not have to have 2 tail assembly chaperone genes. Some can have one. Our evidence for phage Laila is that it has one. When we originally called these genomes, we assumed 2. I think that little gene between the TAC and TMP, gene 14, is real, but not necessarily a tail assembly chaperone (and therefore a hypothetical protein). Make sense? thanks for the question! debbie

Link to this post | posted 17 Apr, 2019 20:50
debbie	Thanks Claire!

Link to this post | posted 16 Apr, 2019 18:43
debbie	i haven't found it either.

Link to this post | posted 16 Apr, 2019 15:17
debbie	We can ask Claire about the glitch. Yes, you can still transfer data from PECAAN into DNA Master for your final file. debbie

Link to this post | posted 13 Apr, 2019 18:58

debbie

Sally, I asked Graham, and he agrees we can call these RexA and RexB. I think that RexA and RexB are a sufficient name. I would not include toxin/antitoxin because it is a known abortive infection mechanism. Toxin/antitoxin is too broad and we know the specifics. For the official list, would you confirm that gene 41 is the RexA and gene 43 is the RexB? (or what genes they are when you re-number?) Cool! debbie